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- PDB-1h45: R210G N-TERMINAL LOBE HUMAN LACTOFERRIN -

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Basic information

Entry
Database: PDB / ID: 1h45
TitleR210G N-TERMINAL LOBE HUMAN LACTOFERRIN
ComponentsLACTOFERRIN
KeywordsMETAL TRANSPORT / IRON TRANSPORT / METAL BINDING
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / humoral immune response / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / protein serine/threonine kinase activator activity / secretory granule / innate immune response in mucosa / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / antibacterial humoral response / heparin binding / positive regulation of NF-kappaB transcription factor activity / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin ...Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPeterson, N.A. / Anderson, B.F. / Jameson, G.B. / Tweedie, J.W. / Baker, E.N.
CitationJournal: Biochemistry / Year: 2002
Title: "Dilysine Trigger" in Transferrins Probed by Mutagenesis of Lactoferrin: Crystal Structures of the R210G, R210E, and R210L Mutants of Human Lactoferrin
Authors: Peterson, N.A. / Arcus, V. / Anderson, B.F. / Tweedie, J.W. / Jameson, G.B. / Baker, E.N.
History
DepositionOct 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1953
Polymers37,0791
Non-polymers1162
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.720, 58.890, 57.530
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LACTOFERRIN


Mass: 37079.070 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE, RESIDUES 20-353 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): BHK / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P02788
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIRON BINDING TRANSPORT PROTEINS THAT CAN BIND TWO FERRIC IRONS IN ASSOCIATION WITH THE BINDING OF ...IRON BINDING TRANSPORT PROTEINS THAT CAN BIND TWO FERRIC IRONS IN ASSOCIATION WITH THE BINDING OF AN ANION LIKE BICARBONATE. BELONGS TO THE TRANSFERRIN FAMILY. ENGINEERED MUTATION ARG 230 GLY CHAIN A
Has protein modificationY
Sequence detailsREGARDING THE SEQUENCE MISMATCH AT RESIDUE 28, THE SEQUENCE THAT WAS USED IN THIS WORK IS FROM THE ...REGARDING THE SEQUENCE MISMATCH AT RESIDUE 28, THE SEQUENCE THAT WAS USED IN THIS WORK IS FROM THE SEQUENCING OF A CDNA FOR HUMAN LACTOFERRIN AND IS THAT GIVEN IN THE FOLLOWING PAPER: ANDERSON BF, BAKER HM, NORRIS GE, RICE DW AND BAKER EN. STRUCTURE OF HUMAN LACTOFERRIN: CRYSTALLOGRAPHIC ANALYSIS AND REFINEMENT AT 2.8 A RESOLUTION. J.MOL.BIOL. 1989. 209 711-734. THE MISMATCH AT 137 IS DERIVED FROM THE REMOVAL OF THE CARBOHYDRATE CHAIN FROM THE RECOMBINANT LACTOFERRIN USING A MIXTURE OF THE ENZYMES ENDOGLYCOSIDASE F AND PEPTIDE N-GLYCOSIDASE F FROM FLAVOBACTERIUM MENINGOSEPTICUM. THIS REACTION LEAVES A CARBOXYL GROUP AT THE GLYCOSYLATION SITE, SO RESIDUE 137 WAS BUILT AS ASP INSTEAD OF ASN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growpH: 8 / Details: HEPES, NACL, pH 8.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128 mg/mlprotein11
220 mMHEPES11
31 M11pH8.0NaCl

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 27857 / % possible obs: 94.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.6
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 4.2 / % possible all: 60.4
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 2.8 %
Reflection shell
*PLUS
% possible obs: 60.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCT

1lct


Resolution: 1.95→30 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1351 4.9 %RANDOM
Rwork0.222 ---
obs0.222 27786 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8612 Å2 / ksol: 0.313589 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.35 Å20 Å20.69 Å2
2--6.36 Å20 Å2
3----12.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 5 92 2599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 167 4.7 %
Rwork0.302 3360 -
obs--72.6 %
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 26435 / Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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